With snow falling throughout, Daniel Lopez swept in from close range in the second minute but Chris Hackett's penalty and Carlisle's header were enough to see the Cobblers move into the automatic promotion places.
There were only 78 seconds on the clock when Lopez tucked home from six yards, after Adam Mekki took the ball wide of Cobblers keeper Lee Nicholls and picked out his team-mate.
But with 21 minutes gone referee Darren Deadman pointed to the spot after Michael Hector handled in the box and Hackett dispatched his spot-kick into the top-right corner.
Hackett then turned provider with ten minutes remaining in the first half, whipping in a corner which Carlisle headed home.
Northampton could have sealed the points with 15 minutes to go after Hackett rounded Jamie Young but his goalbound shot was stopped by Troy Brown.
Jake Robinson's effort was then cleared off the line by Shots substitute Anthony McNamee as Dean Holdsworth's side failed to find a late equaliser.
